# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 20:41:20 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (2~{R})-2-(4-fluorophenyl)-2-[[(2~{S})-2-methyl-3-sulfanyl-propanoyl]amino]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CS)C(=O)N[C@@H](C(O)=O)c1ccc(F)cc1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 8PL  8PL  '(2~{R})-2-(4-fluorophenyl)-2-[[(2~{S})-2-methyl-3-sulfanyl-propanoyl]amino]ethanoic acid'  ligand  31  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8PL
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 8PL  C01  C  CH1    0  -0.225  -0.6451  -0.5644  -0.8488
 8PL  C02  C  CR6    0   0.087  -1.9084  -0.0599  -0.2020
 8PL  C03  C  CR16   0  -0.314  -3.0645   0.1394  -0.9485
 8PL  C04  C  CR16   0  -0.397  -4.2399   0.5797  -0.3539
 8PL  C05  C  CR6    0   0.511  -4.2394   0.8234   1.0045
 8PL  C06  C  CR16   0  -0.396  -3.1115   0.6377   1.7815
 8PL  C07  C  CR16   0  -0.272  -1.9506   0.1902   1.1695
 8PL  F08  F  F      0  -0.318  -5.3693   1.2549   1.5909
 8PL  N09  N  NH1    0  -0.634   0.4277   0.3796  -0.6338
 8PL  C10  C  C      0   0.588   1.6581   0.1516  -1.1141
 8PL  O11  O  O      0  -0.505   1.8953  -0.7079  -1.9516
 8PL  C12  C  CH1    0  -0.389   2.7566   1.0228  -0.5231
 8PL  C13  C  CH2    0  -0.537   3.4615   0.1697   0.5363
 8PL  S14  S  S2     0  -0.258   4.5799   1.2196   1.5248
 8PL  C15  C  CH3    0  -0.648   3.7085   1.5187  -1.6026
 8PL  C16  C  C      0   0.410  -0.3261  -1.9762  -0.2656
 8PL  O17  O  O      0  -0.584   0.4956  -2.0309   0.6630
 8PL  O18  O  OC    -1  -0.599  -0.9785  -2.9064  -0.7716
 8PL  H1   H  HCH1   0   0.251  -0.8212  -0.6659  -1.9224
 8PL  H2   H  HCR6   0   0.262  -3.0527  -0.0465  -2.0152
 8PL  H3   H  HCR6   0   0.278  -5.1356   0.7344  -0.9413
 8PL  H4   H  HCR6   0   0.279  -3.1391   0.8306   2.8461
 8PL  H5   H  HCR6   0   0.264  -1.0702   0.0233   1.7784
 8PL  H6   H  HNH1   0   0.398   0.3274   1.0548   0.1068
 8PL  H7   H  HCH1   0   0.262   2.3011   1.8833  -0.0227
 8PL  H8   H  HCH2   0   0.285   2.7278  -0.2923   1.1965
 8PL  H9   H  HCH2   0   0.269   4.0356  -0.6233   0.0559
 8PL  H10  H  HSH1   0   0.226   5.0067   0.2708   2.3651
 8PL  H11  H  HCH3   0   0.240   3.1804   2.1073  -2.3531
 8PL  H12  H  HCH3   0   0.236   4.4847   2.1530  -1.1755
 8PL  H13  H  HCH3   0   0.229   4.1959   0.6838  -2.1051

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 8PL  C15  C12  single    1.522  0.020  1.522
 8PL  C12  C10  single    1.521  0.020  1.521
 8PL  C12  C13  single    1.532  0.020  1.532
 8PL  F08  C05  single    1.344  0.020  1.344
 8PL  O11  C10  double    1.223  0.020  1.223
 8PL  C06  C05  aromatic  1.382  0.020  1.382
 8PL  C06  C07  aromatic  1.387  0.020  1.387
 8PL  C10  N09  single    1.340  0.020  1.340
 8PL  C05  C04  aromatic  1.380  0.020  1.380
 8PL  C07  C02  aromatic  1.395  0.020  1.395
 8PL  C04  C03  aromatic  1.389  0.020  1.389
 8PL  N09  C01  single    1.445  0.020  1.445
 8PL  C02  C03  aromatic  1.390  0.020  1.390
 8PL  C02  C01  single    1.506  0.020  1.506
 8PL  C13  S14  single    1.825  0.020  1.825
 8PL  C01  C16  single    1.560  0.020  1.560
 8PL  C16  O17  deloc     1.241  0.020  1.241
 8PL  C16  O18  deloc     1.244  0.020  1.244
 8PL  C01  H1   single    0.970  0.020  1.090
 8PL  C03  H2   single    0.930  0.020  1.080
 8PL  C04  H3   single    0.930  0.020  1.080
 8PL  C06  H4   single    0.930  0.020  1.080
 8PL  C07  H5   single    0.930  0.020  1.080
 8PL  N09  H6   single    0.860  0.020  1.020
 8PL  C12  H7   single    0.970  0.020  1.090
 8PL  C13  H8   single    0.970  0.020  1.090
 8PL  C13  H9   single    0.970  0.020  1.090
 8PL  S14  H10  single    1.200  0.020  1.300
 8PL  C15  H11  single    0.970  0.020  1.090
 8PL  C15  H12  single    0.970  0.020  1.090
 8PL  C15  H13  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 8PL  H1   C01  C16  108.43  3.000
 8PL  H1   C01  N09  109.06  3.000
 8PL  C16  C01  N09  112.56  3.000
 8PL  H1   C01  C02  108.53  3.000
 8PL  C16  C01  C02  108.30  3.000
 8PL  N09  C01  C02  109.87  3.000
 8PL  C07  C02  C03  118.49  3.000
 8PL  C03  C02  C01  120.98  3.000
 8PL  C07  C02  C01  120.51  3.000
 8PL  H2   C03  C04  119.03  3.000
 8PL  H2   C03  C02  119.69  3.000
 8PL  C04  C03  C02  121.28  3.000
 8PL  H3   C04  C05  120.61  3.000
 8PL  H3   C04  C03  120.89  3.000
 8PL  C05  C04  C03  118.49  3.000
 8PL  F08  C05  C06  118.94  3.000
 8PL  C06  C05  C04  122.00  3.000
 8PL  F08  C05  C04  119.06  3.000
 8PL  H4   C06  C07  120.87  3.000
 8PL  H4   C06  C05  120.55  3.000
 8PL  C07  C06  C05  118.59  3.000
 8PL  H5   C07  C06  118.82  3.000
 8PL  H5   C07  C02  120.03  3.000
 8PL  C06  C07  C02  121.15  3.000
 8PL  H6   N09  C10  117.96  3.000
 8PL  H6   N09  C01  118.26  3.000
 8PL  C10  N09  C01  121.13  3.000
 8PL  C12  C10  O11  121.89  3.000
 8PL  O11  C10  N09  122.88  3.000
 8PL  C12  C10  N09  115.23  3.000
 8PL  H7   C12  C15  109.16  3.000
 8PL  H7   C12  C13  108.25  3.000
 8PL  C15  C12  C13  112.59  3.000
 8PL  H7   C12  C10  109.10  3.000
 8PL  C13  C12  C10  106.38  3.000
 8PL  C15  C12  C10  111.26  3.000
 8PL  H9   C13  H8   108.24  3.000
 8PL  H9   C13  S14  109.53  3.000
 8PL  H8   C13  S14  109.17  3.000
 8PL  H9   C13  C12  110.03  3.000
 8PL  H8   C13  C12  110.19  3.000
 8PL  S14  C13  C12  109.65  3.000
 8PL  H10  S14  C13   97.34  3.000
 8PL  H13  C15  H12  107.95  3.000
 8PL  H13  C15  H11  108.24  3.000
 8PL  H12  C15  H11  107.50  3.000
 8PL  H13  C15  C12  110.93  3.000
 8PL  H12  C15  C12  110.92  3.000
 8PL  H11  C15  C12  111.17  3.000
 8PL  O18  C16  O17  128.23  3.000
 8PL  O18  C16  C01  114.66  3.000
 8PL  O17  C16  C01  117.05  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 8PL  CONST_01  C05  C06  C07  C02    0.00  0.0  0
 8PL  CONST_02  C05  C04  C03  C02    0.00  0.0  0
 8PL  CONST_03  C06  C05  C04  C03    0.00  0.0  0
 8PL  CONST_04  C06  C07  C02  C03    0.00  0.0  0
 8PL  CONST_05  C07  C06  C05  C04    0.00  0.0  0
 8PL  CONST_06  C07  C02  C03  C04    0.00  0.0  0
 8PL  CONST_07  C06  C07  C02  C01  180.00  0.0  0
 8PL  CONST_08  C04  C03  C02  C01  180.00  0.0  0
 8PL  CONST_09  F08  C05  C04  C03  180.00  0.0  0
 8PL  CONST_10  F08  C05  C06  C07  180.00  0.0  0
 8PL  CONST_11  H4   C06  C07  C02  180.00  0.0  0
 8PL  CONST_12  H3   C04  C03  C02  180.00  0.0  0
 8PL  CONST_13  H5   C07  C02  C03  180.00  0.0  0
 8PL  CONST_14  H2   C03  C04  C05  180.00  0.0  0
 8PL  CONST_16  O11  C10  N09  C01    0.00  0.0  0
 8PL  CONST_17  H6   N09  C10  O11  180.00  0.0  0

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 8PL  chir_01  C01  N09  C02  C16  positiv
 8PL  chir_02  C12  C13  C10  C15  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 8PL  plan-1  C01  0.020
 8PL  plan-1  C02  0.020
 8PL  plan-1  C03  0.020
 8PL  plan-1  C04  0.020
 8PL  plan-1  C05  0.020
 8PL  plan-1  C06  0.020
 8PL  plan-1  C07  0.020
 8PL  plan-1  F08  0.020
 8PL  plan-1  H2   0.020
 8PL  plan-1  H3   0.020
 8PL  plan-1  H4   0.020
 8PL  plan-1  H5   0.020
 8PL  plan-2  C01  0.020
 8PL  plan-2  N09  0.020
 8PL  plan-2  C10  0.020
 8PL  plan-2  O11  0.020
 8PL  plan-2  C12  0.020
 8PL  plan-2  H6   0.020
 8PL  plan-3  C01  0.020
 8PL  plan-3  C16  0.020
 8PL  plan-3  O17  0.020
 8PL  plan-3  O18  0.020

